Proteomics-based identification of differentially expressed genes in human gliomas: down-regulation of SIRT2 gene

AbstractCervical cancer is one of the most common gynecological malignancies. However,studies on the expression and molecular mechanism of miR-205 and miR-141 in CC are insufficient recently. Expression profile microarray with 21329 Oligo DNA were used to detect the expression of mRNAs in miR-205 up-regulated or miR-141 down-regulated HeLa and SiHa cells and mRNAs in normal HeLa and SiHa cells. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were performed to assess the potential pathways of miR-205 in SiHa cell.Compared with normal HeLa cell, there were 38 differentially expressed genes (DEGs) in miR-205 up-regulated HeLa cell. Nine were up-regulation genes and 29 were down-regulation genes. There were 23 DEGs in miR-141 down-regulated HeLa cell. One was up-regulated and 22 were down-regulated. Compared with normal SiHa cell, there were 128 DEGs in miR-205 up-regulated SiHa cell. One hundred and three were up-regulation genes and 25 were down-regulation genes. There were 80 DEGs in miR-141 down-regulated SiHa cell. Forty two were up-regulation genes and 28 were down-regulation genes. For miR-205 up-regulated SiHa cell, GO outcome showed that “ubiquitin-protein ligase activity”, “MAP kinase phosphatase activity”, were the most enriched terms (P < 0.05). And in KEGG analysis, “Cell cycle” was notably enriched, and Smad4 in this pathway was up-regulated (P < 0.05). Expression profile microarray technology can effectively screen out DEGs in cervical cancer cells after up-regulating miR-205 or down-regulating miR-141. Which may enable us to understand the pathogenesis and lay an important foundation for the prevention and treatment of cervical cancer.

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A transcriptomic analysis of sugarcane response to Leifsonia xyli subsp. xyli infection

PLoS ONE ◽

10.1371/journal.pone.0245613 ◽

2021 ◽

Vol 16 (2) ◽

pp. e0245613

Author(s):

Kai Zhu ◽

Li-Tao Yang ◽

Cheng-Xi Li ◽

Prakash Lakshmanan ◽

Yong-Xiu Xing ◽

...

Keyword(s):

Cell Wall ◽

Protein Phosphorylation ◽

Differentially Expressed Genes ◽

Plant Pathogen ◽

Significant Inhibition ◽

Differentially Expressed ◽

Down Regulation ◽

Sugarcane Varieties ◽

Obligate Pathogen ◽

Plant Pathogen Interactions

Sugarcane ratoon stunting disease (RSD) caused by Leifsonia xyli subsp. xyli (Lxx) is a common destructive disease that occurs around the world. Lxx is an obligate pathogen of sugarcane, and previous studies have reported some physiological responses of RSD-affected sugarcane. However, the molecular understanding of sugarcane response to Lxx infection remains unclear. In the present study, transcriptomes of healthy and Lxx-infected sugarcane stalks and leaves were studied to gain more insights into the gene activity in sugarcane in response to Lxx infection. RNA-Seq analysis of healthy and diseased plants transcriptomes identified 107,750 unigenes. Analysis of these unigenes showed a large number of differentially expressed genes (DEGs) occurring mostly in leaves of infected plants. Sugarcane responds to Lxx infection mainly via alteration of metabolic pathways such as photosynthesis, phytohormone biosynthesis, phytohormone action-mediated regulation, and plant-pathogen interactions. It was also found that cell wall defense pathways and protein phosphorylation/dephosphorylation pathways may play important roles in Lxx pathogeneis. In Lxx-infected plants, significant inhibition in photosynthetic processes through large number of differentially expressed genes involved in energy capture, energy metabolism and chloroplast structure. Also, Lxx infection caused down-regulation of gibberellin response through an increased activity of DELLA and down-regulation of GID1 proteins. This alteration in gibberellic acid response combined with the inhibition of photosynthetic processes may account for the majority of growth retardation occurring in RSD-affected plants. A number of genes associated with plant-pathogen interactions were also differentially expressed in Lxx-infected plants. These include those involved in secondary metabolite biosynthesis, protein phosphorylation/dephosphorylation, cell wall biosynthesis, and phagosomes, implicating an active defense response to Lxx infection. Considering the fact that RSD occurs worldwide and a significant cause of sugarcane productivity, a better understanding of Lxx resistance-related processes may help develop tools and technologies for producing RSD-resistant sugarcane varieties through conventional and/or molecular breeding.

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Down-regulation of EPB41L4A-AS1 mediated the brain aging and neurodegenerative diseases via damaging synthesis of NAD+ and ATP

10.21203/rs.3.rs-927236/v1 ◽

2021 ◽

Author(s):

Tingpeng Yang ◽

Yanzhi Wang ◽

Weijie Liao ◽

Shikuan Zhang ◽

Songmao Wang ◽

...

Keyword(s):

Gene Expression ◽

Neurodegenerative Diseases ◽

Differentially Expressed Genes ◽

Brain Aging ◽

Differential Expression Analysis ◽

Differentially Expressed ◽

Gene Clustering ◽

Down Regulation ◽

Nicotinamide Riboside ◽

Age Related

Abstract Background: Long noncoding RNA EPB41L4A-AS1 plays a very important role in metabolism. Aging and neurodegenerative diseases are typical metabolic-related processes. As a metabolism-related lncRNA, EPB41L4A-AS may be involved in the development of brain aging and neurodegenerative diseases. In this study, we aim to reveal the mechanism of EPB41L4A-AS in aging and neurodegenerative diseases.Methods: Age-related differential expression analysis was applied on the gene expression profile of the hippocampus in the Genotype-Tissue Expression database to obtain age-related differentially expressed genes and the weighted correlation network analysis algorithm was used to construct a gene co-expression network for age-related differentially expressed genes to obtain different gene clustering modules. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, protein-protein interaction network, and correlation analysis were used to reveal the mechanism of EPB41L4A-AS1. The mechanism was verified using Gene Expression Omnibus profile GSE5281 and biology experiments (construction of cell lines, Real-time quantitative PCR, Western blot, measurement of ATP and NAD+ levels, nicotinamide riboside treatment, Chromatin Immunoprecipitation) in neurons and glial-derived cells.Results: EPB41L4A-AS1 is down-regulated in aging and Alzheimer’s disease. EPB41L4A-AS1 related genes are genes of the electron transport chain and NAD+ synthesis pathway. Furthermore, these genes are highly related to neurodegenerative diseases and EPB41L4A-AS1 has a positive correlation with them. In addition, biology experiments proved that the down-regulation of EPB41L4A-AS1 can reduce the expression of these genes via modification of the acetylation of lysine 27 on histone 3, resulting in the down-regulation of NAD+ and ATP levels, while the overexpression of EPB41L4A-AS1 and nicotinamide riboside treatment can restore the levels of NAD+ and ATP.Conclusions: Down-regulation of EPB41L4A-AS1 not only disturbs NAD+ biosynthesis but also affects ATP production. As a result, the high demand of brain for NAD+ and ATP can not be met, which promotes the development of brain aging and neurodegenerative diseases. However, overexpression of EPB41L4A-AS1 and nicotinamide riboside, a substrate of NAD+ synthesis, can reduce EPB41L4A-AS1 down-regulation mediated decrease of NAD+ and ATP synthesis. Our results provide a new perspective on brain aging and neurodegenerative diseases.

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